Musa L. was previously separated into five sections (Eumusa, Rhodochlamys, Callimusa, Australimusa and Ingentimusa) based on basic chromosome numbers and morphological characters. However, several molecular analyses currently support restructuring of Musa species into two sections, Musa and Callimusa. The application of simple sequence repeat molecular marker analysis to Musa phylogeny provided valuable, supplemental information about the classification of, and relationships between, Musa species and subspecies. Totally, 28 accessions of Musa acuminata Colla subspecies and varieties and 25 accessions of other Musa species were evaluated; 12 primers produced 91 polymorphic bands, polymorphic information content ranged from 0.4473 to 0.8394 (average = 0.7226), indicating that the primers showed a high level of polymorphism. Our results generally agreed with previous phylogenetic analyses based on molecular data. One clade comprised species of sections Australimusa and Callimusa (X= 10/9); most species of sections Eumusa and Rhodochlamys (X= 11) formed the other clade. The relationships between most species were as expected; however, some species did not conform to findings of previous studies. A wide range of variability was observed in the M. acuminata complex. M. acuminata var. chinensis and M. acuminata subsp. 522 showed the most distant relationships to other subspecies: Musa laterita, Musa ornata and Musa velutina clustered with M. acuminata var. chinensis, suggesting that they may constitute a secondary gene pool for the improvement of cultivated bananas. Molecular data indicated that Musa tongbiguanensis Chen You & Yao-Ting Wu, which was observed and described by our research group in Yunnan, China, was a distinct, new species.